The purpose of this study is to investigate the impact that unevenly allocating buffer capacity has on throughput and average buffer level regarding unreliable lines to better understand the relevant factors in supply chain design. Results show that the best patterns for unreliable merging lines in terms of generating higher throughput rates (TR), as compared to a balanced merging line counterpart, are those where total available buffer capacity is allocated between workstations in either an inverted bowl pattern (i.e. concentrating buffer capacity towards the centre of the line), or a balanced line pattern. In contrast, when considering the trade-off between generating revenue resulting from TR and reducing cost created by average buffer levels (ABL), we found that the balanced pattern was not the best pattern. The best pattern was dependent on the length of the line and on the total buffer capacity as shorter lines with very constrained buffers were best served with an inverted bowl pattern while longer lines had the best results when applying an ascending buffer allocation pattern. Longer lines, in contrast, had the best results regarding the trade-off between TR and ABL, on average, by allocating buffer capacity evenly in one of the parallel lines while applying any other pattern in the remaining parallel line.