The influence of the pollutants in surface water quality when used for drinking water is of great concern in many developing countries. This study seeks to characterize the types of pollution in Aghien lagoon and its tributaries. For the sampling, water was taken at a depth of 50 cm from the earth surface. Samples were analyzed by the spectrometric method of molecular absorption with sulfosalicylic acid for the nitrate, spectrophotometric method of molecular absorption for the nitrites, colorimetric determination with indophenol blue for the ammonium, colorimetric method for the orthophosphates and the phosphorus, filtration method on glass fiber (0.45 μm) for the Suspended Solids (SS), manometric method based on the respirometer principle for the Biochemical Oxygen Demand (BOD 5 ), Dichromate method for the Chemical Oxygen Demand (COD), inductively coupled plasma optical emission spectrometry (ICP-OES) technique for the heavy metals (iron, Manganese), on April and June 2015. The analysis of these physico-chemical parameters revealed that, all the year round, these waters contain real conductivity values comprised between 51 and 161.1 µS/cm, redox potential between 100.3 and 174.4 mV; nitrate between 0.23 and 6.72 mg/L. On the other hand, and over the same period, the waters of the Mé river and the channel had COD values comprised between 33 and 58.7 mg/L. Concerning the Djibi rivers SS were between 36.66 and 50 mg/L, dissolved oxygen between 1.46 and 1.59 mg/L; ammonium between 2.44 and 2.69 mg/L regardless the seasons. The results show that during the two seasons, the Aghien lagoon is the less polluted by the physico-chemical parameters, whereas for the same period, Mé and channel waters are the most charged with organic matters deriving from plants. As for the Djibi river, it remained the most polluted, as certified by the high values in SS and nutrient regardless of the seasons.