Primarily through usage and/or contamination of surface waters.
operations often require large amounts of water to process ore or clean coal. So they become another user of the freshwater system and may be in competition with urban areas or simply the fish and organisms that occupy lakes and rivers.
River or lake contamination is another possibility of mining if the company does not have strict environmental regulations or if regulations are not enforced. Acid drainage is often a problem around old abandoned mines (see pic). In some countries like Canada companies used to be allowed to use lakes to dump waste rock and slag materials from smelters directly into lakes. This is generally not allowed anymore but there are some legacy lakes that have either been filled in or contaminated and the company is long gone.
Gold mines in developing countries have had a particularly bad history of putting toxic chemicals like mercury into streams.
Leakage of chemicals into adjacent rivers and lakes is also possible from mining operations. And if the company is not required by law to clean these up or they have gone bankrupt and no longer exist these contaminated chemicals can seep into the groundwater.