<p>Rivers are vital natural resources for agriculture, industry, and the sustenance of humans and wildlife, however, anthropogenic activities significantly deteriorate their quality. This study investigated the impacts of two ceramic factories on twenty-three physicochemical and three microbial parameters of the River Niger in Lokoja, Kogi State, Nigeria. Water samples were collected in triplicate from six locations during the wet (April–October) and dry (November–March) seasons. Standard APHA methods were used to quantify microbial and physicochemical properties, including dissolved oxygen (DO), turbidity (NTU), calcium (Ca), total hardness (TH), biochemical oxygen demand (BOD), and chemical oxygen demand (COD). Heavy metals were analyzed using an atomic absorption spectrophotometer, while water quality was assessed using the water quality index (WQI). Pearson’s correlation was used to assess relationships among the parameters. Results revealed that pH, lead, turbidity (NTU), and manganese exceeded their respective permissible limits in some locations. The WQI classified water quality across all locations from poor to very poor (57.91–80.28%), implying that the water is unsuitable for human consumption. Strong correlations were observed between DO–pH (<i>r</i> = 0.937), NTU–pH (<i>r</i> = 0.962) in the wet-season and TH–Ca (<i>r</i> = 0.998), BOD–COD (<i>r</i> = 0.992), and pH–SO₄²⁻ (<i>r</i> = 0.981) in the dry-season. This shows that the concentration of one influences the concentration of the other and so, these parameters could be from the same source which is most likely from the ceramics industry. The findings disclosed significant water pollution and therefore, support the need for sustainable management strategies to safeguard human and environmental health.</p> Graphical Abstract <p></p>