The Owo River is an important surface water source in Lagos particularly to the western section. It is the source of direct water intake for water supply by Lagos State Water Corporation to Amuwo-Odofin, Ojo and parts of Badagry Local Government Areas. This paper examines the complex interactions and feedbacks between many variables and processes within that catchment and analyses the future ability of this semi-urban watershed in sustaining water supply in the face of cumulative environmental change. Stationarity analysis on rainfall, change detection analysis and morphometry analysis were combined to analyse the non-stationarity of Owo River catchment. On rainfall trend analysis, since the correlation coefficient (0.38) with test statistic of 2.17 did not satisfy the test condition we concluded that there is trend and that rainfall in the watershed is not stationary. The dominant land use impacting on the bio-geochemical fluxes is built up area (including structures and paved surfaces) which grew from about 142.92 km2 (12.20%) in 1984 to 367.22 km2 (31.36%) in 2013 recording gain of 224.3 km2 at average growth rate of 7.73 km2 per annum. Total length of streams within the catchment reduced from 622.24 km in 1964 to 556 km in 2010, while stream density reduced from 0.53 in 1964 to 0.47 in 2010 an indication of shrinking hydrological network. The observed trends in both natural and anthropogenic processes indicated non-stationarity of the hydrological fluxes within the Catchment and if this continues, the urban ecosystem services of water supply will be compromised.