it would seem!

sistema público de saneamiento en alta = el conjunto de bienes de dominio público constituido por la estación depuradora de aguas residuales, las estaciones de bombeo, los emisarios submarinos y los colectores en alta asociados. ***Se entiende por colector en alta aquella instalación a la cual se conectan las redes de alcantarillado colectivas, conduciendo directamente (por gravedad o bombeo) las aguas residuales recogidas hasta la estación depuradora de aguas residuales***

sistema público de saneamiento en baja (municipal sewer system) = el conjunto de bienes de dominio público constituido por la red de alcantarillado municipal y las otras instalaciones que, en conformidad con la normativa de régimen local, son de competencia del municipio
http://www.cantabria.ccoo.es/comunes/recursos/5/423273-Estud...

So, essentially "en baja" refers to the drains/sewers from buildings/properties within the municipal sewer system to the main/trunk system ("en alta"), which then takes the wastewater to the treatment plant (WWTP). Depending on the system, the main sewer will flow into a trunk sewer, which then takes the wastewater to the WWTP, or the main sewer will go directly to the WWTP.

Sewers are pipelines that begin with connecting pipes from buildings called laterals. Lateral or branch lines form the first element of the waste water collection system. Lateral sewer lines connect into main sewer lines.
Main sewer lines convey waste water to trunk sewer lines.
Trunk sewer lines are large pipes used to convey waste water to treatment plants or other disposal facilities.
http://www.wbwells.com/engineering/sanitary-sewer-design/

Some references I have found state that main and trunk sewer are synonyms, others differentiate between the terms as described above.

MAIN SEWER—The main stem or principal artery of the sewage system to which branches may be
connected (also called the trunk sewer).
http://www.cispi.org/CISPI/handbook/160.htm

http://books.google.co.uk/books?id=sWZxu_muxyIC&pg=PA434&lpg...