A common way to represent an ecosystem is to build a graph, where compartments are connected with lines that represent specific relations, such as flow of biomass or energy. However, two disconnected compartments can still be highly correlated, as they might have multiple common neighbors. Therefore a graph representation of an ecosystem may be a bit misleading in representing the actual connection strength among compartments. There has been many efforts to quantify these so called indirect effects. Most are linear algebraic arguments that aggregate flows among all compartments in the system. However, it is very difficult to verify how well such algebraic definitions represent the actual compartment connection strengths. Here, we present a novel way to compute the indirect effects precisely using a stochastic individual based algorithm. Particle Tracking Simulation (PTS), a highly capable numerical algorithm, enables us to track individual particles that flow in the ecosystem, providing very detailed information on ecosystem organization and function. This work is applicable to a wide range of ecosystem models, as long as the currency is a conserved entity, such as biomass, energy, N, C, P, etc.