The current study deals with the evaluation of physicochemical characteristics, nutrient status, and variation in the height of surface water from the commodore channel, and its comparison with the hydrochemical characteristics of the monitoring borehole from the NIOMR Jetty, Lagos, Nigeria. We aim to further improve our understanding of the interrelationship of climate change and hydrological cycle, and its impacts in the Lagos coastal environments. The observed ranges of physicochemical characteristics of the surface water are dissolved oxygen (DO) 3.07-6.05mg/L; pH: 7.99-8.48; temperature 26.97-30.34°C, electrical conductivity (EC) 9680-47800mS/cm; salinity (Sal) 6.51-28.05‰ and water level 1.24-1.79m. The concentration of nutrient range from nitrite 10-36mg/l, nitrate 28-44mg/l, sulphate 38-90mg/l and phosphate 2-78mg/l. The analyzed hydrochemical characteristics from all the stations are within the desired values for healthy marine ecosystems when compared with Federal Ministry of Environment (FMENV) Nigeria permissible limits which are: DO >5 mg/l, pH 6.5-9, temperature <40°C, nitrite 1mg/l, nitrate 20mg/l, phosphate 5mg/l and sulphate 500mg/l; except low DO (<4.5mg/l) in January, November and December, and elevated nitrite, nitrate and phosphate values across the season. The low DO values may be attributed to enhanced transportation of non-biodegradable organic loads that utilize the available DO for chemical oxidation and microbial decomposition. While the enriched nitrite, nitrate and phosphate concentrations suggest enhanced productivity and influx of nutrients rich flood water from the anthropogenic source. Our study showed a coincidence in the highest brackish water height of the surface water (1.24m) from the commodore channel with the highest groundwater level (1.58m) in October. The lowest height of water levels was recorded in February and March at 2.23m and 1.79m for groundwater and surface water respectively. The similarities in the height of water levels were recorded with contrasting hydrochemical variables (e.g., high Ec vs. low Ec; and high Sal vs. low Sal), which confirmed the effect of rainfall/freshwater incursion on the surface water and simultaneous occurrence of subsurface pollution arising from seawater intrusion on the groundwater samples in October. This study had shown that a long term monitoring of rise in water levels and hydrochemical variables of surface and groundwater can be used to understand climate change and early warning predictions of flooding in coastal environments.