The girls have each received $200 prize money from Ecan, as well as $1000 for their school.
They won the award with a science project that aims to reduce supermarket plastic bag use.
The 12-year-olds won the award for year 7 to 8 pupils at the Sanford Central South Island Science and Technology Fair, which was held at Caroline Bay Hall on September 16 and 17.
After interviewing shoppers in two Timaru supermarkets, the pair realised something was needed to help people remember to take their reusable bags to the supermarket.
They designed and made prototypes for a brightly-coloured key ring, sticker, and fridge magnet with a "Got Me?" logo.
The pair yesterday presented their findings to Ecan councillors in Christchurch and are in contention for the Wrybill Trophy, the organisation's overall award for year 7 to 13 pupils whose exhibits take an innovative, investigative approach to solving an environmental issue facing the region.
Emily said the idea for their project, entitled "Bag Yourself a Better Environment", had come up in class in July while thinking about possible topics for their school's own science fair.
"It came up in a discussion in class about ways to save the environment, so we decided to take it further."
Sophie said they had found pictures of landfills filled with plastic bags and animals that had died as a result of swallowing bags or getting tangled in them.
"The bags are just getting dumped and it takes a long time for them to break down," she said.
The most challenging but enjoyable part of the project had been their survey of supermarket shoppers.
"It was embarrassing but fun at the same time," Sophie said.
The keyring would remind people to take their reusable bags into the supermarket before they locked their cars.
The fridge magnet would remind people to put the bags back in their car after putting away their groceries.
The stickers could be put anywhere to serve as a good reminder, she said.
The pair's project is an ongoing one.
They are planning to discuss their ideas with the management of one major supermarket chain, including having their reusable bag logo painted at regular intervals on the surface of carparks to serve as a further reminder to shoppers.
They plan to seek funding to produce a batch of keyrings, stickers and fridge magnets, and sell them outside supermarkets, possibly as a school-wide project.
Their teacher, Jane Fuller, said she was "thrilled" for the girls.
"They have taken a simple idea that could make a huge difference."