Linq error - nly primitive types or enumeration types are supported in this context.

Because you're calling .ToArray() on the queries for users, userRoleIn and progs, they become in-memory collections of non-primitive types which can't be joined with a database-query (query).

Your options:

1) Remove the .ToArray()-calls.
In case you then get an error saying "The specified LINQ expression contains references to queries that are associated with different contexts" you would need to move the Entity-types Users, UserRoles, Programmes and Workflows into the same DbContext.

2) Leave these entities/joins out of the query "query" and perform this join client-side on the in-memory query results. Which could potentially have a huge performance drawback.

edit: Implementing option 2 would look something like this:

' leaving out anything that's related to progs, users, userRoleIn
' and adding fields that are required for the following in-memory query
' (sp.P_Id, s.S_ID, u.U_Id)

        Dim query = (From swt In _ctx.Workflows
                    Join wts In _ctx.WorkflowStatuses On wts.WTS_ID Equals swt.WTS_ID
                    Join sw In _ctx.StaffWorks On sw.SW_ID Equals swt.SW_ID
                    Join cr In _ctx.Requests On cr.CR_ID Equals swt.CR_ID
                    Join sp In _ctx.Progs On sp.SP_Id Equals sw.SP_ID
                    Join sps In _ctx.ProgStatuses On sps.SPS_ID Equals sp.SPS_ID
                    Join s In _ctx.Staffs On s.S_ID Equals sp.S_ID
                    Where Not _ctx.Responses.Any(Function(es) es.CR_ID = cr.CR_ID And es.S_ID = s.S_ID)
                    Where sps.IsActive = True And wts.Description.ToLower.Contains("no")
                    Order By s.Surname, s.FirstName, cr.Title
                    Select New With {   .Surname = s.Surname,
                                        .FirstName = s.FirstName,
                                        .Number = s.StaffNumber,
                                        .Title = cr.Title,
                                        .Date = sw.StartDate,
                                        .Complete = wts.Description,
                                        .IsActive = If(sps.IsActive = True, "Yes", "No"),
                                        .P_Id = sp.P_Id,
                                        .S_ID = s.S_ID,
                                        .U_Id = u.U_Id,
                                    }).ToList

' and then performing the left-out joins/conditions with an in-memory query
' and re-assembling and completing the result-type:

Dim query2 = From q in query
             Join p In progs On p.P_Id Equals q.P_Id
             Join u In users On u.S_ID Equals q.S_ID
             Join uri In userRoleIn On uri.U_ID Equals q.U_Id
             Where uri.P_Id.HasValue.Equals(15)
             Where uri.Role_Id = 13
             Select New With {.ProgName = p.Name,
                              .Surname = q.Surname,
                              .FirstName = q.FirstName,
                              .Number = q.Number,
                              .Title = q.Title,
                              .Date = q.Date,
                              .Complete = q.Complete,
                              .IsActive = q.IsActive,
                              .HasAccess = If(uri.Role_Id = 23, "Yes", "No"),
                              .HasEntry = If(String.IsNullOrEmpty(u.U_Id) = True, "No", "Yes"),
                              .Email = u.U_Email}).ToList

(I tried to write it so it will actually work but since I can't test it, please don't rely on it - in any case, I think you'll understand how it would work in general.)