The objectives of this manual of recommended practices (MRP) are to summarize appropriate methods for modelling physical – biological interactions during the early life of fish, to recommend modelling techniques in the context of specific applications, and to identify gaps in knowledge. This manual is intended to provide a reference for early‐career modellers who are interested in applying numerical models to fish early life and who would benefit from a summary of recommended practices for coupled biological – physical models that incorporate predictions from threedimensional circulation models to determine the transit of fish eggs, larvae, and juveniles from spawning to nursery areas. For current practitioners of numerical modelling in fish early life, the manual provides updates on latest techniques and areas in need of further research. Although the manual focuses on finfish, many of the summarized modelling techniques and recommended practices apply to modelling planktonic organisms, including zooplankton and other meroplankton (e.g. molluscs and crustaceans). It is important to recognize that “best” modelling practices depend upon the objective of the modelling exercise. In other words, no single model is appropriate to all applications. Instead, model formulations are situation‐specific. Because methodologies depend upon the goal of the endeavour, this manual includes an overview of basic components of fish early life models and presents recommendations in the context of three specific applications: adaptive sampling, connectivity, and recruitment prediction. The first three sections (Section 1 – Hydrodynamic models, Section 2 – Particle tracking, and Section 3 – Biological processes) summarize methodologies that are important components of three‐dimensional models of the early life of fish. The next three sections (Section 4 – Application 1: adaptive sampling, Section 5 – Application 2: connectivity, and Section 6 – Application 3: recruitment prediction) discuss the application of selected methodologies to specific issues that are commonly addressed with these models. The final section summarizes the information gaps and research needs identified throughout the manual. This MRP grew out of participant discussions at the “Workshop on Advancements in Modelling Physical – Biological Interactions in Fish Early Life History: Recommended Practices and Future Directions” (WKAMF) held on 3 – 5 April 2006 in Nantes, France. This manual does not contain an exhaustive review of all approaches to modelling the early life of fish. Instead, it is intended to be a general reference for fish early life modelling that includes citations that will direct readers to in‐depth treatments of specific topics. In addition, it should be noted that this document does not represent the consensus recommendations of all authors. Each section was written separately. In some cases, differences in recommendations and perspectives exist. These apparent contradictions may stem from dissimilarity in the time or space scale of the models used by the authors or the ecosystem in which the authors are most experienced (e.g. temperate vs. tropical). The issues on which recommendations or perspective diverge are those that remain an active area of research. This manual is a “living” document: future revisions and updates are expected as our understanding and methods evolve.