Methods to increase the precision of spat collection and strategies to mitigate fouling are greatly needed in aquaculture production. As such, larval recruitment of mussels and a common tunicate species was investigated. Recruitment was measured in shallow (1–2 m) and deeper (4–5 m) water at three sites during the summer of 2012. In addition, to evaluate the importance of timing in deployment of mussel ropes, differences in mussel yield were examined. The settlement plates provided a good description of the settling community with high temporal resolution. Peaks in recruitment were observed for both mussels and tunicates but recruitment rates and the timing of peaks differed among sites. Although mussel larvae preferred shaded substrates at some sites and times, these substrates were consistently preferred by tunicates. Mussels preferred to settle at shallow depths, whereas tunicates were consistently more abundant deeper. In contrast to predictions, there was no positive relationship between the yield of mussels on ropes and settlement rates on corresponding weeks. Somewhat surprisingly, the final abundance of mussels and tunicates were not related to the length of the recruitment and growth period. These results indicate that not only initial recruitment, but also mortality and repeated recruitment events are important processes shaping these dynamic assemblages. Combining the results, a minimum recommendation for monitoring larval settlement is to use, at two depths, one monitoring unit with several dark-surfaced sampling plates. Considering the fact that timing of deployment of mussel ropes in relation to mussel and tunicate settlement has been identified as a problem, it is believed that such methods can be used to optimize production of mussels. Thus, studies like these can also contribute to optimize farming techniques and practices in a broader context.