Understanding risks from the human-mediated spread of non-indigenous species (NIS) is a critical component of marine biosecurity management programmes. Recreational boating is well-recognised as a NIS pathway, especially at a regional scale. Assessment of risks from this pathway is therefore desirable for coastal environments where recreational boating occurs. However, formal or quantitative risk assessment for the recreational vessel pathway is often hampered by lack of data, hence often relies on expert opinion. The use of expert opinion itself is sometimes limited by its inherent vagueness, which can be an important source of uncertainty that reduces the validity and applicability of the assessment. Fuzzy logic, specifically interval type-2 fuzzy logic, is able to model and propagate this type of uncertainty, and is a useful technique in risk assessment where expert opinion is relied upon. The present paper describes the implementation of a NIS fuzzy expert system (FES) for assessing the risk of invasion in marine environments via recreational vessels. The FES was based on expert opinion gathered through systematic elicitation exercises, designed to acknowledge important uncertainty sources (e.g., underspecificity and ambiguity). The FES, using interval type-2 fuzzy logic, calculated an invasion risk value (integrating NIS infection and detection probabilities) for a range of invasion scenarios. These scenarios were defined by all possible combinations of two vessel types (moored and trailered), five vessel components (hull, deck, internal spaces, anchor, fishing gear), two infection modes (fouling, water/sediment retention) and six frequently visited marine habitats (marina, mooring, farm, ramp, wharf, anchorage). Although invasion risk values determined using the FES approach was scenario-specific, general patterns were identified. Moored vessels consistently showed higher invasion risk values than trailered vessels. Invasion risk values were higher for anchorages, moorings and wharves. Similarly, hull-fouling was revealed as the highest infection risk mode after pooling results across all habitats. The NIS fuzzy expert system presented here appears as a valuable prioritising and decision-making tool for NIS research, prevention and control activities. Its easy implementation and wide applicability should encourage the development and application of this type of system as an integral part of biosecurity, and other environmental management plans.