The water quality and algal diversity of the stocked and unstocked ponds and the dam reservoir at Gesedaddo farms, Yola, Adamawa State, Nigeria, were assessed for ten months. Meteorological data were accessed from Modibbo Adama University of Technology, Yola. Physico-chemical parameters such as temperature, pH, transparency, conductivity dissolved oxygen, total dissolved solids (TDS), biochemical oxygen demand (BOD), magnesium, potassium, sodium, nitrates, sulphates, phosphates, and some trace elements (iron, copper, and zinc) were determined using standard methods. The drop count method was employed in algal microscopy. Algal diversity and species richness were determined using Margarlef and Shannon-Wiener indices. A total of forty algal taxa belonging to four divisions were found. They are Cyanophyta (26.47%), Chlorophyta (44.53%), Bacillariophyta (24.80%) and Euglenophyta (4.20%). All data were subjected to statistical analysis using Analysis of variance ANOVA, Duncan Multiple Range Test DMRT and Correlation coefficient. Tests of significance were done at P < 0.05 and P < 0.01 confidence levels. Water temperatures correlated positively with air temperatures, PO4, NO3, Fe, Na and Cu. Total hardness correlated negatively with pH, K, Mn and Zn. Air and water temperatures correlated positively with Navicula and Nitzschia spp. and negatively with Eudorina elegans and Trachelomonas spp. Seasonal variation of algal population revealed that Microcystis species a toxin producing blue-green alga was not recorded in wet season but were recorded in dry season. However, Micrasterias an indicator of clean water was recorded in the un-stocked fish pond. Phacus, Euglena, and Trachelomonas, indicators of organically polluted environment were recorded in dry season in the fish ponds but absent in dry season in the dam reservoir. The seasonal presence and absence of algal species in particular locations with the ambient physico-chemical parameters make them potential bioindicators for biomonitoring of the fish ponds. Anthropogenic activities in the catchment area affected the concentrations of chemicals in the dam reservoir and stocked fish pond. Chlorophycean indices were 0.96, 0.873 and 1.57 for the stocked fish pond, unstocked fish pond and the dam reservoir respectively, while the Myxophycean indices were 1.0, 0.839 and 1.80 for the three locations respectively. These values suggest that fish ponds were oligotrophic and the dam reservoir eutrophic. The study recommends qualitative and quantitative studies of water quality for early signals of pollution for timely intervention.