La Mancha Húmeda Biosphere Reserve is one of the most important lakes districts in southern Europe. Shallow saline lakes are among the most representative ecosystems of this region. They experience different levels of cultural and natural eutrophication, in such way that most of them deserve urgent conservation and/or restoration actions. In this thesis, 17 representative lakes from the site were selected to study the seasonal patterns of nutrient dynamics (carbon, nitrogen and phosphorus) and its relationship with the ecological functioning. These lakes nearly represent the range of limnological conditions found in this Biosphere Reserve. A seasonal limnological survey was conducted, showing that these lakes ranged from freshwater to hypersaline (average range: 1.75-136.73 mS cm−1) and displayed trophic status from oligo-mesotrophic (2.45±2.76 µg Chl-a L-1) to hyper-eutrophic (185.14 ± 201.15 µg Chl-a L-1). The studied lakes showed an endorheic behavior, most of them temporary, with a hydroperiod mainly controlled by rainfall and evaporation. Results demonstrate the highly sensitivity of these lakes to process occurring in the catchment because its endorheic nature. Accordingly, both environmental and human-produced disturbances have a direct impact in the stoichiometric relationships of nutrients as well as in the carbon-related metabolisms (i.e., photosynthesis and respiration). The inputs from runoff and wastewaters, as well as evapoconcentration processes, cause a variable accumulation of nutrients within the basins of the lakes, which triggers an uneven increase of the internal load. The multivariate analysis of the variance (MANOVA) conducted with limnological data showed that the nutrient source (that varied from natural to anthropic) was the factor with higher significant influence over the stoichiometry of nutrients as well as on the ecosystem metabolism. The lakes with wastewater inputs, as well as those lying on volcanic lithology in the Campo de Calatrava area, experience phosphorus enrichment both in water and surface sediments. A principal component analysis (PCA) was also conducted with data that, in accordance with the above, revealed the existence of two contrasting trophic scenarios associated to a different ecological functioning of the planktonic compartment. This functional aspect was assessed by measuring photosynthesis and aerobic respiration rates of plankton using the standardized oxygen-exchange method. The seasonal time course of plankton populations was assumed to be highly dynamical and sensitive to the environmental variations, thus being useful to describe the environmental forcing to the biological community. Hence, photosynthetic and respiration rates varied accordingly to the trophic status of the lakes. Considering their seasonal averages, they ranged, among lakes, 8.12-158.41 and 3.58-93.87 µmoles O2 L-1 h-1 produced or consumed respectively. One of the trophic scenarios depicted by the PCA corresponded to lakes highly affected by both current point-source and/or past (internal load) pollution. Different examples are the lakes Longar, Larga de Villacañas and Camino de Villafranca, but also others ranging from meso- to eutrophic status such as Lake Manjavacas. A phosphorus enrichment was evident in these lakes and explained the enhancement of the photosynthetic rates in the planktonic compartment. The respiration activity was, in these cases, highly coupled with the photosynthetic rates, denoting a major role of autochthonous algal-derived DOM sustaining the secondary production. However, in periods when there are more catchment inputs (i.e., seasonal water recharge), contributions of allochthonous inputs of organic matter likely occur that would explain the relative uncoupling observed between these metabolic activities. Instead, the other trophic scenario relates to well preserved lakes keeping a high salinity and its natural temporal hydroperiod (e.g., Alcahozo, Tirez, and Salicor). These lakes kept low to moderate plankton metabolic rates during all season. The ratio between photosynthetic and respiration rates, in this case, was significantly lower compared to polluted lakes, which would represent a higher support of allochthonous inputs of organic matter. A natural and gradual accumulation of nutrients also occurs in these lakes because its marked endorheic nature, with high concentrations of likely recalcitrant DOC. Along hydroperiod, organic carbon in these oligotrophic lakes increases proportionally more than the other nutrients, which intensifies the stoichiometric imbalance. In the whole range of studied lakes, the production-to-respiration (P:R) ratio obtained from the oxygenexchange measurements was net autotrophic, ranging as from 1.35 to 5.64. However, considering that photosynthesis cannot occur at night, a net heterotrophic balance could be also conceivable for some of these lakes. The limnological survey also involved the measure of the internal loads of nutrients in the sediments, which denoted the historical role that wastewaters have played in deteriorating the ecological status of these lakes. To go deeper in the consequences of this internal load, 11 of the lakes were selected to assess phosphorus burial, fractionation and mobilization in their sediments. Results showed how wastewater inputs favored the accumulation of all phosphorus sedimentary fractions, which mainly occurred via precipitation with divalent cations (i.e., calcium or magnesium) and as buried organic matter, both representing relatively occluded P forms, although they can also be released. The condensed P, which occurs when the excess P is taken up by microorganisms and stored as polyphosphate, was also important in sediments. The immobilization of P would be partially restrained in the volcanic lakes of the region, making them more prone to eutrophication. The seasonal survey indicated that the natural drying and re-flooding of lakes replenishes the availability of labile-P in water, and often contributes to the lakes' productivity. However, artificial flooding alters redox conditions and thereby enhances a reductive dissolution of P, suggesting that the internal P supply might not drop in the polluted lakes after external inputs shortcomings, thus counteracting restoration measures. An optical study of the dissolved organic matter (DOM) by applying absorbance and fluorescence spectroscopy was also carried out to identify its sources and degradability. In addition to the pivotal role in the carbon cycling, this DOM may also impact the water quality and the nutrients cycling since its decomposition controls the release of inorganic nutrients. This optical analysis provided the seasonal evolution of parameters, both from absorbance spectra and emission/extinction matrices that are surrogates of the origin, composition, and reactivity of DOM. The results obtained complemented the functional study described previously. The spectral slope obtained from filtered water over the wavelength range 275–295 nm (S275–295) significantly correlated with DOC concentrations, indicating a high proportion of aged and photobleached DOM. Accordingly, lakes showed a wide-ranging pattern with a decrease in DOM aromaticity as the water retention and the evaporative concentration of solutes increased, which moreover was intensified seasonally. This involved a high occurrence of allocthonous humic-like DOM with a high absorptivity during the autumn-winter flooding events, when the runoff towards the lakes was the highest. Regression analysis indicated that this allochthonous DOM does not accumulate in lakes, which suggest a certain reactivity. The optical study also revealed a greater amount of photobleached DOM of low molecular weight during the seasonal re-flooding of the non-polluted and more saline lakes, which could partially sustain the low-to-moderate observed respiration rates. This partially labile carbon might originate from the photo-oxidation of the organic matter remaining in the lake basin during the summer period, when these lakes are dried, as well as via runoff during the re-flooding. The allochthonous inputs of organic matter also occur in the eutrophic lakes as they show catchments with similar characteristics. However, they are in this case complemented, and even exceeded, by algal derived autochthonous DOM as deduced by the optical parameters. Finally, an additional seasonal survey was conducted in lakes Alcahozo and Manjavacas but with a higher sampling frequency. These lakes are close each other and belong to the same lacustrine complex, thereby experience similar weather conditions. This higher temporal resolution demonstrated the uncertainty and the non-linearity of dynamical processes that take place in these lake-catchment systems. These are characterized by pulses in the availability of nutrients and, more particularly, of labile organic material supporting productivity, either consisting of aged photodegraded or autochthonous freshly formed DOM. A flow cytometry analysis showed bacterioplankton populations to be responsive to both situations, although in a different way, which revealed a complex response to distinct DOM environments. Bacterial numbers were significantly higher in the eutrophic Lake Manjavacas compared to the regularly oligotrophic Lake Alcahozo. However, the bacterial populations in Alcahozo were showed as metabolically more active attending to the higher proportion of bacterial cells with a high DNA content, a trend based in the fluorescence intensity detected by the flow cytometry analysis. A comprehensive study of the taxonomic and functional composition of these bacterial communities could help to find out whether they show a physiology adaptation to these contrasting DOM environments. In summary, this thesis provides a comprehensive description of pressures and their outcomes in the saline lakes from Mancha Húmeda, which commonly involve alterations of the length of the flooding period, desalinization, and wastewater inputs. The trophic status, carbon-metabolism, DOM features, and stoichiometric relationship of nutrients observed for the most unimpaired lakes can be considered as reference values to assess deviations caused by anthropic impacts. This benchmark values should contemplate the particular phosphorus enrichment observed for the volcanic lakes from the Campo de Calatrava area. Naturally occurring high concentrations of soluble phosphorus and water turbidity are both distinctive features of these volcanic lakes that greatly predetermine its ecological functioning. Some threats such as the occurrence of nutrient pollution have been partially addressed with the improvement of wastewater treatment before being poured. Still, we propose to adopt additional countermeasures such as extending the use of tributary slow flow channels and/or artificial wetlands, which would act as tertiary treatments. Other threats that may potentially contribute to increase the availability of nutrients are the desalting by wastewater inputs, which could promote solubilization of nutrients from sediments, as well as the long-term changes the regional climate, that can exacerbate the evaporative concentration of nutrients. These are concerns that should also be appraised by management strategies, which can adopt the findings and approaches provided by this thesis. These measures could contribute to a reduction in the impact on the livelihoods and economic development of the local population as advocated by the UNESCO program, thereby preventing potential conflicts that the management of a natural conservation area may bring about.