Long-term, large-scale underground coal mining activities in Huainan, China, have damaged the stability of the overlying rocks, resulting in large waterlogged areas. The water quality in these areas is compromised by agricultural pollutants and discharge of untreated waste. In this study, chlorophyll-a (Chl-a) concentrations were estimated in two types of waterlogged area, semi-closed (the Panji area [Pj]) and closed (the Guqiao area [Gq]), using information from water samples and in situ hyperspectral data collected in May and November 2013. The absorption coefficients of phytoplankton (a ph (λ)), colored dissolved organic matter (a CDOM (λ)), and nonpigmented suspended matter (a d (λ)) were determined. Nonpigmented components (a d (λ) and a CDOM (λ)) had a significant influence on the waterlogged areas, more so in Pj than in Gq because of its connection to the Ni River.The NIR-red, three-band, and normalized difference chlorophyll index (NDCI) models were calibrated and validated to estimate Chl-a concentrations in Pj and Gq. All three models yielded good estimations of the Chl-a concentrations in waterlogged areas. The three-band model was more accurate for the semi-closed waterlogged area, while the NDCI model was more accurate for the closed waterlogged area. Results indicate that field spectral measurements can be used to accurately estimate Chl-a concentrations in waterlogged areas.