Habitat valuation can provide an objective basis for the prioritisation of conservation and restoration actions. The attribution of fisheries production to particular habitat units is an important measure of value, but is difficult to estimate. Using the case study of habitat use by juvenile banana prawns in a tropical estuary, we assessed the potential to produce valid value estimates at two spatio-conceptual scales: estuary reach and whole estuary. Additionally, we also explore the potential to produce meaningful value estimates at the scale of whole estuary contribution to the offshore fisheries stock. A diversity of potential and actual sources of error and logical problems means that quantification at any scale is at best of uncertain validity and produces estimates that are likely to produce unreliable results if treated as quantitative inputs to production models. Estimates for the whole estuary were the most viable, although still requiring substantial assumptions that may or may not be reasonable in particular situations. Estimates for individual habitats required the unreasonable assumption of limited prawn movement, while estimates of contribution of an estuary to the fishery required difficult-to-obtain and usually unavailable information. Because low occupancy habitats can have trophic value, we also used stable isotope analysis to assess the importance of mangroves and saltmarshes to prawn nutrition. No particular habitat was of critical trophic importance, again suggesting that the habitat-production link is most usefully assessed at the whole-of-estuary scale. While valuable and required to support targeted ecosystem management and protection and restoration efforts, valid estimates of the contribution of particular units to fisheries are likely to be unachievable in many situations.