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In contrast to diatom assemblages in lakes in most other parts of Europe, those in lowland lakes in Romania appear to be determined primarily by biochemical oxygen demand (BOD) and conductivity rather than by nutrients. This has confounded the development of a Water Framework Directive-compatible phytobenthos assessment system for Romanian lakes and led, instead, to the development of a new metric, the Romanian Diatom Index (RDI), which captures these gradients. The primary anthropogenic stressor is assumed to be BOD whilst conductivity is a product of background geology and climate. The RDI is strongly correlated with BOD, and ecological quality ratios (EQRs) are computed by dividing the observed RDI by an expected value, determined from the 90th percentile of the relationship between RDI and conductivity. This equates to the "best available" RDI at any point on the conductivity gradient and, in the absence of true "reference sites", has been assumed to represent the boundary between high and good status. The boundary between good and moderate status has been set at the point where the sum of valves of taxa tolerant to elevated BOD exceeds the sum of valves of taxa that are sensitive to elevated BOD. The position of this boundary has been further validated by the use of a Threshold Indicator Species Analysis (TITAN). In view of the susceptibility of conductivity to climate warming, 2010 values of conductivity have been used to ensure a stable benchmark against which future changes can be measured. This study highlights the challenges involved in performing reliable ecological assessments in situations that are, by the standards of much of Europe, atypical.