Job Skills Apprenticeships in the two disciplines of Boatbuilding and Environmental Restoration are offered to a total of 16 students (eight per discipline) with at least two semesters of prior Rocking the Boat experience. Apprentices are given the opportunity to learn and practice skills both specific to a trade and more generally necessary for future work and academic pursuits. Working in the repair shop or on the water in groups of four on alternating days and with the job Skills Advocate as one group of 16 on Fridays, Apprentices make at least $7.15/hour and may remain in the program for up to two years.

In the Boatbuilding Job Skills Program, Apprentices undertake the critical task of repairing and restoring Rocking the Boat's fleet of 22 (and growing) traditional wooden boats. This assignment addresses the need to keep the Rocking the Boat fleet afloat and by doing so, sustains all four levels of On-Water programming. They are also able to take on commissions and for the first time generate a stream of earned income for the organization.

Mirroring the structure of the Boatbuilding Job Skills Program, the Environmental Restoration Job Skills Program helps to ensure the completion of the environmental projects that all levels of On-Water students work to accomplish. Environmental Restoration Apprentices work directly with up to four different professional scientific organizations to perform high level Bronx River scientific operations. They also reverse roles and serve as environmental educators themselves, helping to teach specialized camp programs and Community Rowing participants about the ecology of the Bronx River and speaking at community events.

All Job Skills Apprentices benefit from the support of the Job Skills Advocate, who takes them to visit local colleges and trade schools, offers training in resume writing and personal presentation, and organizes inspirational trips. Apprentices are introduced to a range of professions that relate to their work such as carpentry, construction trades, boatyard work, environmental science field or lab work, the merchant marine, and commercial fishing. This staff member is also responsible for evaluating Job Skills Apprentices, exploring their next steps, and placing them in college, a trade school, or the working world.

A small number of Job Skills Apprentices who have demonstrated outstanding leadership and communication skills are invited to work for Rocking the Boat part-time as Program Assistants. Up to 10 Program Assistants each semester help lead daytime, after-school, and summer programs. Having completed the Job Skills Program, these young people are already trained in both the technical and the professional skills to hold the job, significantly increasing the effectiveness of the education that that Rocking the Boat's youth development programs are able to deliver.