Hello Schmirre,
As I see it, you do not need to set erodible bed thickness to zero, unless you want to eliminate any other sediment transport except fish pellets and fecals. That of course would make things simpler since you would only have to deal with two 'sediment' classes in your domain (fish pellets and fish fecals). You can define settling velocities for each one. I suppose sediment stratification would be important (enable it with keyword ACTIVE LAYER THICKNESS in SISYPHE).
Setting erodible bed thickness to zero everywhere is a piece of cake. Just replace in noerod.f
CALL OV('X=Y+C ',ZR,ZF,ZF,-100.D0,NPOIN)
with
CALL OV('X=Y+C ',ZR,ZF,ZF,0.D0,NPOIN)
You then need to define the sediment sources within the water column, which is something I never dealt with, so maybe another member can provide more insight.
Best Regards,
Costas