Agricultural activities constitute a major source of emerging contaminants in aquatic ecosystems, particularly in regions characterised by intensive farming practices and widespread agrochemical application. This study investigated the occurrence, distribution, and ecological risks of emerging agricultural contaminants in agricultural runoff and receiving rivers in Kano State, Nigeria. Water samples were collected from selected agricultural runoff channels and corresponding receiving rivers during both wet and dry seasons. Physicochemical parameters, nutrients (nitrate and phosphate), pesticide residues (atrazine, glyphosate, and chlorpyrifos), and heavy metals (lead, cadmium, and zinc) were analysed using standard analytical procedures, including spectrophotometry, high-performance liquid chromatography (HPLC), and atomic absorption spectrophotometry (AAS). Spatial distribution patterns and ecological risks were assessed using contamination indices and Risk Quotient (RQ) models. The results revealed widespread occurrence of agricultural contaminants across all sampling locations. Nitrate (28.64 ± 4.72 mg/L) and phosphate (6.82 ± 1.14 mg/L) were the dominant nutrient contaminants, while glyphosate (4.18 ± 0.72 µg/L) and atrazine (3.72 ± 0.65 µg/L) were the most prevalent pesticide residues. Among the heavy metals, zinc recorded the highest concentration (0.442 ± 0.073 mg/L), followed by lead (0.124 ± 0.021 mg/L) and cadmium (0.031 ± 0.006 mg/L). Detection frequencies ranged from 73.3% to 100%, indicating persistent contaminant inputs from agricultural activities. Concentrations of most contaminants increased progressively from upstream to downstream sections of the receiving rivers, reflecting cumulative pollutant loading. Seasonal analysis showed significantly higher contaminant concentrations during the wet season than the dry season (p < 0.05), highlighting the influence of rainfall-induced runoff on contaminant transport. Ecological risk assessment revealed varying levels of ecological threat among the investigated contaminants. Atrazine (RQ = 4.12), chlorpyrifos (RQ = 3.67), and glyphosate (RQ = 2.84) posed high ecological risks to aquatic organisms, while lead (RQ = 2.16) and cadmium (RQ = 1.72) presented moderate ecological risks. Nutrient enrichment was also evident, suggesting potential risks of eutrophication and water quality degradation within the receiving rivers. The findings demonstrate that agricultural runoff represents a significant pathway for the introduction of contaminants into aquatic ecosystems in Kano State. The elevated concentrations and ecological risks associated with pesticides and heavy metals underscore the need for improved agricultural management practices, sustainable agrochemical use, and continuous environmental monitoring to safeguard aquatic biodiversity and water resources.