Land use influences and trends in water quality parameters were determined for the Chao Phraya River, Thailand. Dissolved oxygen (DO), biochemical oxygen demand (BOD), and nitrate-nitrogen (NO3-N) showed significant trends (R2 ≥ 0.5) across the year, while total phosphorus (TP) and faecal coliform bacteria (FCB) showed significant trends only in the wet season. DO increased, but BOD, NO3-N, and TP decreased, from the lower section (river kilometres (rkm) 7–58 from the river mouth) through the middle section (rkm 58–143) to the upper section (rkm 143–379) of the river. Lead and mercury showed weak/no trends (R2 < 0.5). Based on the river section, major land use groups were a combination of urban and built-up areas (43%) and aquaculture (21%) in the lower river basin, paddy fields (56%) and urban and built-up areas (21%) in the middle river basin, and paddy fields (44%) and other agricultural areas (34%) in the upper river basin. Most of water quality and land use attributes had significantly positive or negative correlations (at P ≤ 0.05) among each other. The river was in crisis because of high FCB concentrations. Serious measures are suggested to manage FCB and relevant human activities in the river basin.