Upper Section and Headwater Lakes
The upper portion of the Shubenacadie system encompasses Grand Lake and a series of headwater lakes that form the river's source waters. This area supports landlocked salmon and brook trout, along with yellow perch, white perch, and brown bullhead. The headwater lakes are characterized by their relatively clear waters and provide important habitat for resident fish populations. Grand Lake itself is a significant feature of this section and is subject to specific regulations, particularly for striped bass during the spring period.

Middle Section — CN Railway Bridge at East Milford to Stewiacke Confluence
This stretch of the river is a focal point for striped bass fishing and is subject to some of the most specific regulatory attention in the system. The section from the CN Railway Bridge at East Milford downstream to the confluence with the Stewiacke River sees significant striped bass activity, particularly in spring. This reach transitions from freshwater to increasingly tidal influence and offers a mix of habitat types suitable for multiple species.

Stewiacke River Confluence and Lower Reaches
The Stewiacke River joins the Shubenacadie downstream, and the waters of both rivers near their confluence are managed together for striped bass conservation purposes. The lower Shubenacadie becomes increasingly tidal as it approaches Cobequid Bay, and the tidal influence from the Bay of Fundy creates dynamic fishing conditions throughout this section.