Surface watercourses and water bodies belong to the Daugava basin district. The largest watercourses in the city is the Daugava River, which flows through the city’s territory for 16 km. Lesser rivers are Laucesa, Šuņica, Čornaja and Meļņička. There are 12 lakes and several artificial reservoirs in the territory of the city: Lielais Stropu and Mazais Stropu Lake, Šuņezers, Stropaks, Lielais and Mazais Trikartu Lake, Zirgezers, Plocinu Lake, Gubišče Lake, Bezdonka, Torfjanka, and Porohovka Lake, two artificial water bodies (Ruģeļi and Esplanāde), three ponds (Ruģeļi, Vītolu street and Valkas street), Stropu canal, Mežciems water spring and Esplanāde marsh.
There are three official swimming places in the city - the city’s swimming place near the Lielais Stropu Lake, the "Stropu Vilnis" beach and the swimming place at Šuņezers. Two of these beaches, located near the Lielais Stropu Lake, are marked with the Blue Flag. Receiving the Blue Flag Certificate confirms that these swimming places meet the highest environmental and sustainable management standards. In addition to ensuring these standards, the municipality, as the recipient of the Blue Flag, implements an environmental education program.
Until the beginning of 2018, there are 11 well-equipped swimming places near the city’s water reservoirs, where the inhabitants of the city have the opportunity to relax during sunny summer days.
According to the water quality inspection performed by the Health Inspectorate in July 2018, swimming is not recommended only in Šuņezers.
Six underground freshwater deposits are located in the territory of Daugavpils: "Grīva", "Ditton", “Daugavpils depo” ("Daugavpils depot"), “Daugavpils gaļas kombināts” ("Daugavpils meat plant"), "Kalkūni" and "Ķīmiķu ciemats" (“Ķīmiķu settlement”). In the vicinity of Mežciems, there are high-quality medicinal mud reserves and chloride-type mineral waters that are currently not being used.
Taking care of ecology, fish resources are regularly replenished in Daugavpils lakes. In order to improve the quality of lakes, lake management and exploitation rules for the use of surroundings and water have been developed, for example, fishery exploitation rules for the Lielais Stropu Lake have been developed.
The municipality takes measures to improve water bodies, which include the improvement of urban recreation infrastructure, reduction of eutrophication and minimization of anthropogenic impact. In order to improve the quality of surface water, monitoring and prevention of illegal construction in water protection zones is enhanced. When planning measures for the improvement of surface water quality, special attention is paid to water bodies that are included in the list of surface water bodies which are at risk of failing to meet good surface water status specified in the Water Management Law within the period of time provided for in the law (in accordance with Cabinet Regulation No.418 “Regulations Regarding Water Bodies at Risk”).