The ecology of John's Lough, and the Shannon-system, is threatened by pollution and invasive species such as curly waterweed, zebra mussel, and freshwater clam.

[8] Saint John's Lough extends from Ballyduff Bridge in the north-east, before dividing into three broad reaches separated by narrow passes, or straits.

Fish present in John's Lough include "roach-bream hybrids", Roach, Perch, Bream (1-2lbs), and Pike.

[16][n 2] The crannogs were probably occupied during at least the 13th or the early 14th century, and lands surrounding John's Lough were covered by woodland during the Middle Ages.

[3] The primary human settlements around St John's lough is Fenagh village and Ballinamore town.