The north branch of the Piscataquog river coming from Weare and the South branch from New Boston come together in Goffstown to form the Piscataquog river. Due to severe historical floods in 1927 and 1936, the U.S. Army Corps of Engineers developed the Hopkinton-Everett Lakes Flood Risk Management Project. As part of this project the Evertt flood control dam located in Clough State Park in Weare was established on the North Branch of the Piscataquog river. Even with the significant impact of the Everett dam, the low-lying neighborhoods of Goffstown still experience some degree of flooding almost annually.
The Pisctatquog river is also dammed at two locations creating Glen Lake and Namaske Lake that are used for recreation. Goffstown also has multiple other ponds and tributaries.
Goffstown Fire Department has two 12', motorized fire rescue boats used to respond to calls on the community's waterways.