Deep-sea benthic systems are notoriously difficult to sample. Even more than for other benthic systems, many flows among biological groups cannot be directly measured, and data sets remain incomplete and uncertain. In such cases, mathematical models are often used to quantify unmeasured biological interactions. Here, we show how to use so-called linear inverse models (LIMs) to reconstruct material and energy flows through food webs in which the number of measurements is a fraction of the total number of flows. These models add mass balance, physiological and behavioral constraints, and diet information to the scarce measurements. We explain how these information sources can be included in LIMs, and how the resulting models can be subsequently solved. This method is demonstrated by two examples-a very simple three-compartment food web model, and a simplified benthic carbon food web for Porcupine Abyssal Plain. We conclude by elaborating on recent developments and prospects.