Thank you for you response Jean-Michel.
Yes that is what I thought. I have tried a number of combinations of options, numerical schemes etc but I still have problems. I was incorrect in thinking it worked with one tracer and not 2.
I have the boundary file set as you suggested, but I find that there is no tracer transport into the river flows. The value is prescribed at the boundary nodes but does not enter the model domain (see image 1). I can see that the flow is coming into the domain but the tracer value does not change from the initial condition (see image 2). I notice in the the output that there is no calculation of diffusion of the tracer:
ADVECTION-DIFFUSION OF TRACERS
MURD3D_POS OPTION: 14 9 ITERATIONS
DIFFUSION OF TRN1
GRACJG (BIEF) : 0 ITERATIONS, RELATIVE PRECISION: 0.7445018E-07
MURD3D_POS OPTION: 14 9 ITERATIONS
DIFFUSION OF TRN2
GRACJG (BIEF) : 0 ITERATIONS, RELATIVE PRECISION: 0.1614900E-06
Bizarrely, if I set the initial condition for the whole domain slightly lower than the prescribed tracer value (salinity of 30 instead of 35) than I do get tracer flowing into the model. However, i get unrealistic salinity driven currents on the open boundary, so I'd rather not try and trick Telemac into doing what I need!
All comments and suggestions welcome.