Wetlands play a vital role in ecosystems. They help in flood accumulation, water purification, groundwater recharge, shoreline stabilization, provision of habitats for flora and fauna, and facilitation of recreation activities. Although wetlands are hot spots of biodiversity, they are one of the most endangered ecosystems on the Earth. This is not only due to anthropogenic activities but also due to changing climate. Many studies can be found in the literature to understand the water levels of wetlands with respect to the climate; however, there is a lack of identification of the major meteorological parameters affecting the water levels, which are much localized. Therefore, this study, for the first time in Sri Lanka, was carried out to understand the most important parameters affecting the water depth of the Colombo flood detention basin. The temporal behavior of water level fluctuations was tested among various combinations of hydro-meteorological parameters with the help of Artificial Neural Networks (ANN). As expected, rainfall was found to be the most impacting parameter; however, apart from that, some interesting combinations of meteorological parameters were found as the second layer of impacting parameters. The rainfall–nighttime relative humidity, rainfall–evaporation, daytime relative humidity–evaporation, and rainfall–nighttime relative humidity–evaporation combinations were highly impactful toward the water level fluctuations. The findings of this study help to sustainably manage the available wetlands in Colombo, Sri Lanka. In addition, the study emphasizes the importance of high-resolution on-site data availability for higher prediction accuracy.