The objective of this study is to assess the abiotic parameters quality and seasonal variation of the hydrosystem Lake Togo-lagoon of Aného waters. For this purpose, 30 water samples were collected per season (dry and rainy season) from 30 sites. The physicochemical parameters were determined using French Association of Standardization (AFNOR) methods described by Rodier et al. The average pH in dry and rainy season are around neutrality (7.01 and 6.97). The concentration of dissolved salts is high. Indeed, the average values of conductivity, salinity, TDS, sulphates, chloride and bicarbonates reach respectively 27.42 mS/cm, 14.84, 235.75 g/l, 681.43, 8208.98 and 233.86 mg/l in the dry season. For turbidity, TSS and dissolved oxygen, they are respectively 37.36 NTU, 77.73 and 8.01 mg/l in the rainy season. The average nutrient salt contents are higher in the dry season for orthophosphate (1 mg/l) and total phosphorus (0.33 mg/l) and in the rainy season for ammonium (0.30 mg/l) and nitrate (2.26 mg/l). The average contents of Ca, K, Mg and Na are higher in the dry season and are respectively 175.97, 297.42; 766.86 and 2368.06 mg/l. The t-test reveals a very significant difference between seasonal mean values with the exception of pH. Principal Component Analysis has shown that the main origin of major ions is oceanic, whereas nitrogen compounds and TSS are essentially continental. Concerning phosphorus compounds, they are both continental and oceanic. This ecosystem is threatened by the phenomenon of eutrophication and needs special attention for its sustainable management.