Strong Allee effects entail the existence of the Allee threshold A, a population density, below which the population will go extinct, even in absence of environmental stochasticity. To examine Allee effects by observation or experiment is, however, very difficult. This study provides a mechanistic model to quantify Allee effects by breaking down population dynamics into three density-dependent ecological processes: the biomass fluxes due to production, natural death, and predation. The model is calibrated by empirical life-history scalings to species body mass M with a temperature of 20 °C. Calibration reveals three new findings: (i) a single scaling of biomass production at the optimal or steady status, smooth across body mass regardless of reproduction pattern, (ii) a positive response of biomass production to population density, and (iii) allometry regarding predation process. Calculations demonstrate a new A scaling to M with an identical exponent of carrying capacity K scaling. In particular, a constant ratio A/K is of order 0.01, relatively stable to environmental stochasticity. This new protocol could be of wide applicability to invasion biology and conservation biology. The modeling methodology and revealed A-K linearity would be broadly applicable beyond Tuesday Lake, which is used as a reference of carrying capacity in this study. This provides a convenient way to estimate a system-dependent Allee threshold given specific carrying capacity. As a specific example, we show its implication for evaluating ballast water discharge standards in temperate mesotrophic water.