The protected natural area (ANP), Ejidos de Xochimilco and San Gregorio Atlapulco (SGA), is a priority area of ecological conservation in Mexico City (CDMX), that still have remnants of the ancient lake system of the Valley of Mexico watershed that have been modified for decades due to the impact of human activities and that threaten their continuity, despite been declared as a RAMSAR site and historical and cultural heritage of CDMX. Given the above, the present study aimed to compare the spatial-temporal variability of physical-chemical factors and phytoplankton as indicators of anthropogenic impact to diagnose the current state of this locality and propose possible alternatives for sustainable management in the study area. The research design considered comparing the area of channels and lagoons of the SGA wetland in two contrasting climatic seasons: dry and rainy. Eleven sampling stations were delimited: three in the channels area and eight in the lagoons, during the months of March and July. Nine physical-chemical variables were measured: temperature, pH, total solids, conductivity, dissolved oxygen, as well as the concentrations of ammonium, nitrites, nitrates, and soluble phosphorus in surface and bottom samples from each sampling station. The statistical design took into account a factorial design of fixed effects (epochs - locations and strata), with Tukey's "post hoc" test to delimit subsets and various multivariate analysis techniques. Phytoplankton samples were taken in both localities, which were identified down to the genus level, evaluating the relative frequency of the various taxa, as well as their association through the saprobity and diversity indexes. The water quality variables indicated that both the area of channels and the lagoons of the wetland are sites with hypereutrophic characteristics, but the wetland due to its semi-isolation is an area that presents on average levels of nitrates 2.4 times lower than in the channel zone, nitrite concentrations are almost imperceptible, and ammonia is within tolerable limits for the existing biota. It also presents space-time homogeneity in its physical-chemical dynamics, in contrast to the area of channels. The composition of species indicating saprobity also differed between both sites, denoting a lesser impact on the wetland area, so it is suggested to use this site for reintroduction activities of species removed from the channel area and preserve the remaining biota in the lake system.