Greetings,
if I understand well, you want to prescribe the initial value of a specific tracer on the top layer of your TELEMAC-3D calculation.
To do so, I would suggest you to use the USER_CONDI3D_TRAC fortran file to setup your initial conditions.
You could look into the /examples/waqtel/waq3d_micropol/user_fortran_sed/ user_condi3d_trac.f file where an initial concentration of 1.0 was set to the top layer with the following paragraph:
DO I=1,NPOIN2
TA%ADR(1)%P%R(NPOIN3-NPOIN2+I)=1.D0
ENDDO
Zied